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- PDB-4bz6: Crystal structure of Schistosoma mansoni HDAC8 complexed with SAHA -

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Basic information

Entry
Database: PDB / ID: 4bz6
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with SAHA
ComponentsHISTONE DEACETYLASE 8
KeywordsHYDROLASE / PLATYHELMINTHS / INHIBITION
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / heterochromatin formation / metal ion binding / nucleus
Similarity search - Function
Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIMETHYLFORMAMIDE / : / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / histone deacetylase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarek, M. / Romier, C.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural Basis for the Inhibition of Histone Deacetylase 8 (Hdac8), a Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni.
Authors: Marek, M. / Kannan, S. / Hauser, A. / Moraes Mourao, M. / Caby, S. / Cura, V. / Stolfa, D.A. / Schmidtkunz, K. / Lancelot, J. / Andrade, L. / Renaud, J. / Oliveira, G. / Sippl, W. / Jung, M. ...Authors: Marek, M. / Kannan, S. / Hauser, A. / Moraes Mourao, M. / Caby, S. / Cura, V. / Stolfa, D.A. / Schmidtkunz, K. / Lancelot, J. / Andrade, L. / Renaud, J. / Oliveira, G. / Sippl, W. / Jung, M. / Cavarelli, J. / Pierce, R.J. / Romier, C.
History
DepositionJul 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEACETYLASE 8
B: HISTONE DEACETYLASE 8
C: HISTONE DEACETYLASE 8
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,99927
Polymers201,7804
Non-polymers2,21923
Water16,682926
1
A: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9456
Polymers50,4451
Non-polymers5005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0918
Polymers50,4451
Non-polymers6467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0187
Polymers50,4451
Non-polymers5736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9456
Polymers50,4451
Non-polymers5005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.640, 70.640, 97.990
Angle α, β, γ (deg.)77.88, 75.48, 85.69
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
HISTONE DEACETYLASE 8


Mass: 50444.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PNEA/TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5H660

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Non-polymers , 6 types, 949 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N2O3
#6: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE GSLVPR MOTIF AT THE END OF THE SEQUENCE CORRESPONDS TO A BAMHI CLONING SITE (GS) FOLLOWED BY A ...THE GSLVPR MOTIF AT THE END OF THE SEQUENCE CORRESPONDS TO A BAMHI CLONING SITE (GS) FOLLOWED BY A THROMBIN SITE (LVPR) THAT HAS BEEN CUT AFTER THE ARGININE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 19 % / Description: NONE
Crystal growDetails: 0.2 M NA,K L-TARTRATE, 21% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2→36 Å / Num. obs: 117881 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.5 / % possible all: 96.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T67

1t67


Resolution: 2→34.74 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.9375 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.133
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN K. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=14011. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN K. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=14011. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=12.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 5968 5.06 %RANDOM
Rwork0.1633 ---
obs0.1647 117868 97.34 %-
Displacement parametersBiso mean: 28.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.636 Å2-2.0146 Å2-0.4396 Å2
2--2.4333 Å23.3275 Å2
3----0.7973 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12958 0 127 926 14011
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113442HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9418258HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4461SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes288HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1963HARMONIC5
X-RAY DIFFRACTIONt_it13442HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion16.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1674SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16795SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2048 412 4.94 %
Rwork0.1785 7922 -
all0.1798 8334 -
obs--97.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16610.1827-0.28730.7057-0.37951.02770.0241-0.178-0.06320.0961-0.0532-0.0561-0.00180.08640.029-0.1028-0.0024-0.0218-0.00010.0085-0.10753.409125.073886.341
20.7881-0.16330.13780.3894-0.09930.6263-0.012-0.04350.06-0.0013-0.0093-0.0015-0.043-0.01930.0213-0.07830.0124-0.0046-0.0079-0.0073-0.042988.470743.266970.8241
30.3735-0.1513-0.14221.21920.1920.6002-0.0121-0.0034-0.0126-0.13620.01980.032-0.0356-0.0384-0.0078-0.02820.0068-0.0132-0.05740.0047-0.078844.24242.402741.4458
40.93860.2846-0.53910.9787-0.05741.0878-0.1030.1155-0.1536-0.12140.0181-0.11710.05710.02830.0849-0.0464-0.00760.0323-0.0819-0.0155-0.08564.949235.895125.7599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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